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https://github.com/arjunrajlaboratory/RajLabSeqTools
10 December 2020, 08:13:17 UTC
Revision d6501d6d78c65d29b415c9c8b96298d4d581f418 authored by Arjun Raj on 18 June 2014, 17:12:56 UTC, committed by Arjun Raj on 18 June 2014, 17:12:56 UTC 
Playing with unzip and concatenate fasta.
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Tip revision: d6501d6d78c65d29b415c9c8b96298d4d581f418 authored by Arjun Raj on 18 June 2014, 17:12:56 UTC
Playing with unzip and concatenate fasta.
Tip revision: d6501d6
unzipAndConcatenateZippedFasta.sh 
#!/bin/bash

ZIPFILEDIRECTORY=$1

OUTFASTADIRECTORY=$2

for dirname in $ZIPFIELDIRECTORY/* ; do
    cd $dirname

    INPUT=`ls *001_R1*`
    SAMPLE=`echo $INPUT | cut -d'_' -f 1`

    if [ ! -d $EXPERIMENT/raw ]; then
        mkdir $EXPERIMENT/raw
    fi

    if [ ! -d $EXPERIMENT/raw/$SAMPLE ]; then
        mkdir $EXPERIMENT/raw/$SAMPLE
    fi

    for i in *.gz; do
        gunzip -c $i > ${i%.*}
    done

    FASTQR1=`echo $SAMPLE'_R1.fastq'`
    FASTQR2=`echo $SAMPLE'_R2.fastq'`

    cat *R1*fastq > $EXPERIMENT/raw/$SAMPLE/$FASTQR1
    cat *R2*fastq > $EXPERIMENT/raw/$SAMPLE/$FASTQR2

done
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